Here are a few things I have found on my first glance.
I just noticed that the carrier commands are live on Tribble. I spent an hour today playing with one of the flight deck carriers and trying things out.

Flights stay out and do not de-spawn now.

Summoning flights take far less time now to recharge and launch another flight.

The four current commands are Attack, Guard, Intercept and follow(Recall).

The item in the hanger slot was of blue quality so I guessing we now have several qualities levels

Attack  The flight attacks your currently selected target. It always attacks the current target so if you are flipping through targets your flights will also be jumping with you.

Guard  The flights will defend the selected target. I need to try this one out a little more to see if it is working.

Intercept  The flights are on over watch and will attack other fighters and torps.

Follow  Its a recall order and follow command.

The command powers are a toggle with very little explanation of what your flights should be doing when no toggle is active.

List of bugs:
-Sometimes flights in the Follow command will not switch over to another command.
-Attack and Intercept do not have an auto follow added to the script when no target is selected or when they are awaiting a new command.
-I tried intercept when I was fighting Romulans to kill the torps but they did not shoot them down so Im not sure if it is working at this point.

A few things that are needed:
-Better descriptions on how the commands work and how to use them.
-When you call out another flight to refill your lost numbers it will de-spawn one of the spawned flights and spawn a new one. The issue is that it might also be the same flight that is still at full strength and the second flight that only has one fighter left was not the one swapped out. The way it should work is to spawn more to fill in the missing ranks. Maybe you could add a new power called reinforce that holds a linked cool down to the spawn flight power.
-A recall and dock command for your flights.
-When a flight follows they cluster right next to the ship, easy for an aoe to kill them all. Could we get a set formations that could be selected from for the follow command. First thing comes to my mind are flights from the Homeworld games.
-A follow command added to a number of the other commands as a default action.

If I have stuff wrong I apologize as I only had a quick look at the new system.

There is also an issue where when flights are on recall, they sometimes will not all follow you at full impulse. This causes you to leave some fighters behind. More of a problem with the Vo'quv and Kar'fi since they can have more fighters out, but was definitely an issue when I was using the T3 Orion vessel.